A wide range of human pharmaceuticals are present at low concentrations in freshwater systems, particularly in sections of polluted river. These compounds show high biological activity, often associated with a high stability. These characteristics imply a potential impact of these substances on aquatic biota even when present at low environmental concentrations. Low flow conditions in Mediterranean rivers, most of which flow through densely populated areas and are subjected to intensive water use, increase the environmental risk of these emergent compounds. Here, we studied whether pharmaceuticals in river water affect the local benthic community structure (diatoms and invertebrates). For this purpose, we analyzed the occurrence of pharmaceuticals along the Llobregat River and examined the benthic community structure (diatoms and invertebrates) of this system. Some pharmaceutical products in the Llobregat River registered concentrations greater than those cited in the literature. Multivariate analyses revealed a potential causal association between the concentrations of some anti-inflammatories and β-blockers and the abundance and biomass of several benthic invertebrates (Chironomus spp. and Tubifex tubifex). Further interpretation in terms of cause-and-effect relationships is discussed; however, it must be always taken with caution because other pollutants also may have significant contributions. Combined with further community experiments in the laboratory, our approach could be a desirable way to proceed in future risk management decisions.